Yes, it will. But that filter should contribute very little to the SWR/impedance of what follows it, and shouldn't make any difference anyway. If it does, it's improperly designed, or there's a problem with something on the 'front side' of that filter.
A filter should be placed where it will do the most good. Since whatever's on the front side of that filter is 'dirty' and whatever's behind that filter is 'clean', the closer to the thing that's 'dirty', the better. Right? Less radiation of the unwanted stuff.
That filter (low pass type) can also be a very rough means of finding what's doing the 'dirty' stuff. Placed right after the transmitter and no change in output, then probably something after the transmitter is the culprit (if there's anything 'after' the transmitter, such as an amplifier?). If placed after than amplifier and things 'clean' up, guess what the probable culprit is. If it doesn't 'clean' anything up, beat it to death with a hammer, it don't work anyway. And all that assumes that the problem is with your transmitter/amplifier/whatever, not a problem with the receiving device. That's not a definitive way of testing or checking, just a very rough one, and there's a lot of "if/and/buts" in there... whooopy.
- 'Doc
Don't take the thingy about the hammer too literally. It just makes you feel better about guessing wrong.